The SMARTLAM project proposes a new paradigm of modular, flexible, scalable 3D-Integration (3D-I) scenarios for 3D manufacturing of microsystems out of laminated polymer films. During the integration of discrete parts and laminated polymer sheets, a fast and precise vision system is needed to inspect the top layer of functional elements and align laminated films. A pattern matching vision approach is implemented in this project to assure production quality and detect faults between production processes and/or at the end. The system’s key hardware components are a high-resolution line camera system and an X/Y/Z-axis system for positioning setup. The software architecture of the inspection module builds on a plugin like structure, based on software design pattern criterion, in order to facilitate fast adaptation of algorithms for new updates of manufacturing requirements. The results demonstrate the high ability of the developed vision system to accurately detect features and defects of the laminated polymer films for layers alignments and assurance of in-process and final quality.